Open csmangum opened 5 hours ago
To evaluate the accuracy of your Krebs Cycle simulation using the metabolites listed, you can perform a systematic analysis of several key factors. This involves comparing your simulation results with known biochemical data, checking for consistency in metabolite concentrations, energy yield, and reaction rates. Here’s a step-by-step approach to using these metabolites for validation:
By following these steps, you can systematically evaluate how accurately your simulation represents the biological processes of the Krebs Cycle. This will allow you to identify any discrepancies and refine your model for more realistic simulations.
A tracker can also have validators or checks. Used to analyze the simulation results
Feature Request: Create a
Tracker
Class for Monitoring Simulation MetricsDescription
We need a flexible
Tracker
class that can be inherited by other classes to track specific aspects of the Krebs Cycle simulation. This will enable better organization of tracking logic and allow for modular tracking of different metrics like energy yield, CO₂ production, NAD+/NADH ratios, and more.Goals
Tracker
base class that will serve as a parent for tracking different simulation metrics.Tracker
to monitor specific metrics, such as:Proposed Structure
Tracker
Class:start_tracking()
: Initialize tracking.log_change(metric: str, value: float)
: Log changes in the specified metric.report()
: Generate a summary report of tracked values.reset()
: Reset the tracker for a new simulation run.tracked_metrics
: Dictionary or list to store metric values over time.simulation_step
: Tracks the current simulation step to correlate logs with time.Example Inherited Classes:
EnergyTracker(Tracker)
CO2Tracker(Tracker)
RedoxBalanceTracker(Tracker)
Acceptance Criteria
Tracker
base class is implemented with methods for tracking, logging, and reporting.EnergyTracker
,CO2Tracker
) are implemented for tracking specific simulation metrics.Tracker
class and its child classes, including usage examples and sample outputs.Benefits